Skip to main content
NCBI home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1984 Oct;4(10):2120–2127. doi: 10.1128/mcb.4.10.2120

Identification of a recently evolved goat embryonic beta-globin pseudogene which retains transcriptional activity in vitro.

S G Shapiro, J B Lingrel
PMCID: PMC369030  PMID: 6095041

Abstract

A clone containing the entire goat epsilon V beta-globin gene, which lies downstream from the two tandemly duplicated four-gene sets containing the beta C and beta A genes in the linkage group 5'-epsilon I-epsilon II-psi beta X-beta C-epsilon III-epsilon IV-psi beta Z-beta A-epsilon V-3', was isolated, and the sequence of the gene was determined. epsilon V is most homologous to the first gene in each of these sets, epsilon I and epsilon III, and appears to be a third duplicated copy of these genes, possibly the first gene in a third four-gene set. Homology of epsilon V to epsilon I is very high (93.2%) in coding regions, and all transcription, processing, and potential translation consensus sequence elements appear to be present, although the Hogness box of epsilon V is altered compared with that of epsilon I by the deletion of an A(AATAAAA----AATAAA). Nevertheless, epsilon V is clearly a pseudogene as a result of two deletions and one insertion (or insertion-deletion) in its coding sequence, the first of which produces an in-frame stop codon at amino acid 54. Unlike the more highly mutated goat beta-like pseudogene duplicates psi beta X and psi beta Z, epsilon V acquired its defects after the duplication event in which it was created. Its recently acquired defects have left the epsilon V promoter sufficiently conserved to retain transcriptional activity in vitro. The acquisition of defects by this gene may be related to the multiple gene duplications which have created at least five epsilon type genes in the goat beta-globin locus.

Full text

PDF
2120

Images in this article

2121Image
on p.2121
2125Image
on p.2125

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baralle F. E., Shoulders C. C., Proudfoot N. J. The primary structure of the human epsilon-globin gene. Cell. 1980 Oct;21(3):621–626. doi: 10.1016/0092-8674(80)90425-0. [DOI] [PubMed] [Google Scholar]
  2. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  3. Blattner F. R., Williams B. G., Blechl A. E., Denniston-Thompson K., Faber H. E., Furlong L., Grunwald D. J., Kiefer D. O., Moore D. D., Schumm J. W. Charon phages: safer derivatives of bacteriophage lambda for DNA cloning. Science. 1977 Apr 8;196(4286):161–169. doi: 10.1126/science.847462. [DOI] [PubMed] [Google Scholar]
  4. Breathnach R., Benoist C., O'Hare K., Gannon F., Chambon P. Ovalbumin gene: evidence for a leader sequence in mRNA and DNA sequences at the exon-intron boundaries. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4853–4857. doi: 10.1073/pnas.75.10.4853. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cleary M. L., Haynes J. R., Schon E. A., Lingrel J. B. Identification by nucleotide sequence analysis of a goat pseudoglobin gene. Nucleic Acids Res. 1980 Oct 24;8(20):4791–4802. doi: 10.1093/nar/8.20.4791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cleary M. L., Schon E. A., Lingrel J. B. Two related pseudogenes are the result of a gene duplication in the goat beta-globin locus. Cell. 1981 Oct;26(2 Pt 2):181–190. doi: 10.1016/0092-8674(81)90301-9. [DOI] [PubMed] [Google Scholar]
  7. Coppola J. A., Field A. S., Luse D. S. Promoter-proximal pausing by RNA polymerase II in vitro: transcripts shorter than 20 nucleotides are not capped. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1251–1255. doi: 10.1073/pnas.80.5.1251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dierks P., van Ooyen A., Cochran M. D., Dobkin C., Reiser J., Weissmann C. Three regions upstream from the cap site are required for efficient and accurate transcription of the rabbit beta-globin gene in mouse 3T6 cells. Cell. 1983 Mar;32(3):695–706. doi: 10.1016/0092-8674(83)90055-7. [DOI] [PubMed] [Google Scholar]
  9. Dierks P., van Ooyen A., Mantei N., Weissmann C. DNA sequences preceding the rabbit beta-globin gene are required for formation in mouse L cells of beta-globin RNA with the correct 5' terminus. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1411–1415. doi: 10.1073/pnas.78.3.1411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dolan M., Dodgson J. B., Engel J. D. Analysis of the adult chicken beta-globin gene. Nucleotide sequence of the locus, microheterogeneity at the 5'-end of beta-globin mRNA, and aberrant nuclear RNA species. J Biol Chem. 1983 Mar 25;258(6):3983–3990. [PubMed] [Google Scholar]
  11. Eaton W. A. The relationship between coding sequences and function in haemoglobin. Nature. 1980 Mar 13;284(5752):183–185. doi: 10.1038/284183a0. [DOI] [PubMed] [Google Scholar]
  12. Efstratiadis A., Posakony J. W., Maniatis T., Lawn R. M., O'Connell C., Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M., Slightom J. L. The structure and evolution of the human beta-globin gene family. Cell. 1980 Oct;21(3):653–668. doi: 10.1016/0092-8674(80)90429-8. [DOI] [PubMed] [Google Scholar]
  13. Fantoni A., Farace M. G., Gambari R. Embryonic hemoglobins in man and other mammals. Blood. 1981 Apr;57(4):623–633. [PubMed] [Google Scholar]
  14. Fritsch E. F., Lawn R. M., Maniatis T. Molecular cloning and characterization of the human beta-like globin gene cluster. Cell. 1980 Apr;19(4):959–972. doi: 10.1016/0092-8674(80)90087-2. [DOI] [PubMed] [Google Scholar]
  15. Grosveld G. C., Shewmaker C. K., Jat P., Flavell R. A. Localization of DNA sequences necessary for transcription of the rabbit beta-globin gene in vitro. Cell. 1981 Jul;25(1):215–226. doi: 10.1016/0092-8674(81)90246-4. [DOI] [PubMed] [Google Scholar]
  16. Grosveld G. C., de Boer E., Shewmaker C. K., Flavell R. A. DNA sequences necessary for transcription of the rabbit beta-globin gene in vivo. Nature. 1982 Jan 14;295(5845):120–126. doi: 10.1038/295120a0. [DOI] [PubMed] [Google Scholar]
  17. Hansen J. N., Konkel D. A., Leder P. The sequence of a mouse embryonic beta-globin gene. Evolution of the gene and its signal region. J Biol Chem. 1982 Jan 25;257(2):1048–1052. [PubMed] [Google Scholar]
  18. Hardison R. C., Butler E. T., 3rd, Lacy E., Maniatis T., Rosenthal N., Efstratiadis A. The structure and transcription of four linked rabbit beta-like globin genes. Cell. 1979 Dec;18(4):1285–1297. doi: 10.1016/0092-8674(79)90239-3. [DOI] [PubMed] [Google Scholar]
  19. Hardison R. C. The nucleotide sequence of rabbit embryonic globin gene beta 3. J Biol Chem. 1981 Nov 25;256(22):11780–11786. [PubMed] [Google Scholar]
  20. Hardison R. C. The nucleotide sequence of the rabbit embryonic globin gene beta 4. J Biol Chem. 1983 Jul 25;258(14):8739–8744. [PubMed] [Google Scholar]
  21. Haynes J. R., Rosteck P., Jr, Schon E. A., Gallagher P. M., Burks D. J., Smith K., Lingrel J. B. The isolation of the beta A-, beta C-, and gamma-globin genes and a presumptive embryonic globin gene from a goat DNA recombinant library. J Biol Chem. 1980 Jul 10;255(13):6355–6367. [PubMed] [Google Scholar]
  22. Jahn C. L., Hutchison C. A., 3rd, Phillips S. J., Weaver S., Haigwood N. L., Voliva C. F., Edgell M. H. DNA sequence organization of the beta-globin complex in the BALB/c mouse. Cell. 1980 Aug;21(1):159–168. doi: 10.1016/0092-8674(80)90123-3. [DOI] [PubMed] [Google Scholar]
  23. Jeffreys A. J., Flavell R. A. The rabbit beta-globin gene contains a large large insert in the coding sequence. Cell. 1977 Dec;12(4):1097–1108. doi: 10.1016/0092-8674(77)90172-6. [DOI] [PubMed] [Google Scholar]
  24. Konkel D. A., Maizel J. V., Jr, Leder P. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes. Cell. 1979 Nov;18(3):865–873. doi: 10.1016/0092-8674(79)90138-7. [DOI] [PubMed] [Google Scholar]
  25. Lacy E., Hardison R. C., Quon D., Maniatis T. The linkage arrangement of four rabbit beta-like globin genes. Cell. 1979 Dec;18(4):1273–1283. doi: 10.1016/0092-8674(79)90238-1. [DOI] [PubMed] [Google Scholar]
  26. Lacy E., Maniatis T. The nucleotide sequence of a rabbit beta-globin pseudogene. Cell. 1980 Sep;21(2):545–553. doi: 10.1016/0092-8674(80)90492-4. [DOI] [PubMed] [Google Scholar]
  27. Lawn R. M., Efstratiadis A., O'Connell C., Maniatis T. The nucleotide sequence of the human beta-globin gene. Cell. 1980 Oct;21(3):647–651. doi: 10.1016/0092-8674(80)90428-6. [DOI] [PubMed] [Google Scholar]
  28. Luse D. S., Haynes J. R., VanLeeuwen D., Schon E. A., Cleary M. L., Shapiro S. G., Lingrel J. B., Roeder R. G. Transcription of the beta-like globin genes and pseudogenes of the goat in a cell-free system. Nucleic Acids Res. 1981 Sep 11;9(17):4339–4354. doi: 10.1093/nar/9.17.4339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  30. Perler F., Efstratiadis A., Lomedico P., Gilbert W., Kolodner R., Dodgson J. The evolution of genes: the chicken preproinsulin gene. Cell. 1980 Jun;20(2):555–566. doi: 10.1016/0092-8674(80)90641-8. [DOI] [PubMed] [Google Scholar]
  31. Proudfoot N. J., Brownlee G. G. 3' non-coding region sequences in eukaryotic messenger RNA. Nature. 1976 Sep 16;263(5574):211–214. doi: 10.1038/263211a0. [DOI] [PubMed] [Google Scholar]
  32. Proudfoot N. J., Shander M. H., Manley J. L., Gefter M. L., Maniatis T. Structure and in vitro transcription of human globin genes. Science. 1980 Sep 19;209(4463):1329–1336. doi: 10.1126/science.6158093. [DOI] [PubMed] [Google Scholar]
  33. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  34. Sassone-Corsi P., Corden J., Kédinger C., Chambon P. Promotion of specific in vitro transcription by excised "TATA" box sequences inserted in a foreign nucleotide environment. Nucleic Acids Res. 1981 Aug 25;9(16):3941–3958. doi: 10.1093/nar/9.16.3941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Schon E. A., Cleary M. L., Haynes J. R., Lingrel J. B. Structure and evolution of goat gamma-, beta C- and beta A-globin genes: three developmentally regulated genes contain inserted elements. Cell. 1981 Dec;27(2 Pt 1):359–369. doi: 10.1016/0092-8674(81)90419-0. [DOI] [PubMed] [Google Scholar]
  36. Shapiro S. G., Schon E. A., Townes T. M., Lingrel J. B. Sequence and linkage of the goat epsilon I and epsilon II beta-globin genes. J Mol Biol. 1983 Sep 5;169(1):31–52. doi: 10.1016/s0022-2836(83)80174-0. [DOI] [PubMed] [Google Scholar]
  37. Shen S. H., Slightom J. L., Smithies O. A history of the human fetal globin gene duplication. Cell. 1981 Oct;26(2 Pt 2):191–203. doi: 10.1016/0092-8674(81)90302-0. [DOI] [PubMed] [Google Scholar]
  38. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  39. Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M. Complete nucleotide sequence of the human delta-globin gene. Cell. 1980 Oct;21(3):639–646. doi: 10.1016/0092-8674(80)90427-4. [DOI] [PubMed] [Google Scholar]
  40. Townes T. M., Shapiro S. G., Wernke S. M., Lingrel J. B. Duplication of a four-gene set during the evolution of the goat beta-globin locus produced genes now expressed differentially in development. J Biol Chem. 1984 Feb 10;259(3):1896–1900. [PubMed] [Google Scholar]
  41. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES